School-based empowerment programs are types of interventions targeting students with or without behavioral, psychological, and emotional difficulties at schools. The purpose of the current study was to examine the effectiveness of a school-based social and mental empowerment program on students' behavioral and developmental problems. We hypothesized that providing adolescents with social and emotional skills may result in improved well-being and health. For this study, which involved 1008 students, we recruited 557 students (242 boys and 315 girls) for the intervention group using a cluster sampling. Also, we recruited 451 students (198 boys and 253 girls) for the control group. Students in both groups were administered the Strength and Difficulties Questionnaire (SDQ). The students in the treatment group received fourteen 90-min sessions designed to address psycho-social and health issues in adolescence, while students in the control group received their regular curriculum. In order to analyze the data, analysis of covariance test was used. Consistent with our hypothesis, respondents in the intervention group had lower difficulties as measured by SDQ and higher pro-social behavior (P <0.05). In conclusion, our study showed that the Social and mental Empowerment Program was a structured preventive program and feasible even in low-resource settings. Future studies might benefit from follow-up with participants in the experimental group, as well as including other relevant students' outcomes.